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- Fullmetal Alchemist, though the manga and the 2003 anime adaptation differ in how many people are aware of/involved in the conspiracy. The conspiracy itself is different in the manga and first anime; in the manga, Father and the upper echelons of the military are planning to create a utopia through Human Sacrifice. In the 2003 anime, the conspiracy is Dante using the country (though Pride) to create situations that lead to the creation of Philosopher's Stones (again through mass human sacrifice) that Dante needs to fuel her immortality.
- The .hack series' system administrators work much the same way up until the end of .hack//Legend of the Twilight.
- And afterward as well. CC Corp just never learns.
- Neon Genesis Evangelion: The shadowy SEELE manipulates both the UN and the Japanese government by claiming that they are trying to prevent The End of the World as We Know It, but their true interest is to make sure that the apocalyptic event turns out in their favor.
- Magical Girl Lyrical Nanoha StrikerS. Turns out that The Federation was behind Jail Scaglietti and all his projects.
- The World Government in One Piece comes down hard on anyone who can read poneglyphs, is scheming to get their hands on plans to a Lost Technology superweapon, and keeps a tight lid on the truth behind the "Blank Century" in the world's history. What are they hiding? To a lesser extent, they also quickly spin any story that might paint pirates in a favorable light, or simply embarrasses the World Government. The events of Alabasta, resolved by the Straw Hats, were credited to Smoker because he was the highest ranking Marine there at the time. They would have done the same with Dressrosa, but Admiral Fujitora torpedoed those plans by broadcasting what really happened before the government even knew about it.
- In the past, Nagi's work in Mahou Sensei Negima! was made more difficult by the fact that Fate's group had several secret supporters in the various governments of the Magic World. In the present, considering how one of Nagi's old friends warned our heroes to be wary of Ostia's Governor-General, it seems Negi is in a similar situation as well. That's just the tip of the iceberg. The masterminds behind the attack on Negi's home village were members of the Megalo Mesembria Senate who have been pulling the strings of the Senate since the beginning of the war, which they helped start.
- The manga version of Narutaru has one of these observing the shadow dragons, as well as being involved in a lot of cover-ups and extreme military measures.
- The Gundam series has had a number of these:
- Gundam 0083: Stardust Memory suggests that the Titans came about due to a conspiracy in the Federation government. Namely, Jamitov Hymem knew of Operation Stardust, and willingly played along (without Delaz's knowledge), thinking that the resultant destruction would frighten the Federation into approving an autonomous military force in space. It worked perfectly.
- Gundam SEED has LOGOS, a group of extremely rich weapons manufacturers who spark wars in an effort to keep selling their products. They have several world leaders in their collective pocket. They are also the true leaders of the global terrorist organization Blue Cosmos.
- Celestial Being in Gundam 00 has hundreds, perhaps thousands, of agents in numerous governments and powerful corporations across the world, which explains where their vast information network and funding comes from. Ribbons Almarck starts one in the second season, pulling the strings of the newly-united world government to do whatever he wants.
- Mobile Suit Gundam Unicorn meanwhile reveals that Laplace's Box is this for both the Vist Foundation and the Universal Century as a whole. Especially since the contents would effectively destroy the entire Earth Federation if they were ever revealed.
- Attack on Titan: The walls that surround and protect all that's left of humankind from the Titans have countless Colossal Titans inside of them. Only the royals and the high-ranking members of the Wall Cult know about them, and they keep it secret from all other humans.
- The government has also banned books about the world outside the walls and made it a taboo to even show interest in venturing outside the walls. They also have the military return weapons not made to their specifications, even if the weapon was significantly improved.
- Even worse are the Millitary Police Secret Service, an elite death squad equipped with anti-soldier 3D-Maneuver gear and led by serial killer Kenny Ackerman. They effectively rule the military police and send mp grunts on murder missions. Most of the soldiers in the military police are Just Following Orders but some have taken a liking to the slaughter of civilians whose only crimes were quietly criticizing the government, getting in the way... or making weapons/technology that could better fight the titans. This slowly drives the survey corps (Rebels) insane.
- As it turns out, all of the above is done for one purpose: To ensure the Titans' rule over humanity. The most damning thing is that the ruling Reiss family has had access to a power that could have freed humanity at any time for nearly a century, but did nothing.
- And the reason WHY they're such extreme isolationists? Because everything outside of the Titan continent is 'Naziland. Nazis with blimps and machine guns. It really is death out there.
- Brynhildr in the Darkness: The villains are implied to have powerful contacts in the government because in episode 6 Ryouta is warned that the police will be on the lookout for a Harnessed, meaning they must be in on the whole deal.
- Lupin III: Island of Assassins: The island's location is unmarked on any map, since the world's major governments all have a vested interest in keeping it hidden: because the Tarantulas are their private hit squad. Which is why they have a Kill Sat in place to shoot down anything approaching the island, or attempting to leave it, without authorization. Lupin tells Jigen that it's the secret behind all the disappearances in The Bermuda Triangle.
- Tokyo Ghoul: The leaders of the CCG have been cooperating with a secret organization of ghouls for more than a century, to maintain control over society. It gets worse, though: the elite Investigators trained at a facility known as the Sunlit Garden are actually short-lived Half-Human Hybrid Tyke Bombs, including Kishou Arima himself. And The Clan that has commanded the CCG since it's inception? The famous clan of ghoul hunters tasked by the Emperor with protecting Japan? The Washuu Clan are also ghouls, meaning that the three highest ranked officials within the CCG are themselves ghouls, using human pawns to exterminate any competition or threats to their authority.
- Ikigami: The Ultimate Limit: From the moment you read "Nanomachines in children" you knew there had to be some government plot to control these childrens' futures. And there is: not only can they execute rebels or delinquents at any given time, but the constant threat of government execution while their parents watch instills a mindset that death is always looming and it would be better to die for a cause than die rebelling to the end (something that has been shown up until now in a positive light from the reader's perspective), which makes the consenters eager to willingly sacrifice their lives for their country. Also known as perfectly disposable soldiers. And the kicker? Once the citizens willingly accept their role, the nanomachines are removed before the deadline to instill "grateful loyalty" to the country, replacing the physical shackles with spiritual ones. And it works.
- Martian Successor Nadesico has one that changes the entire purpose of the war: the spacebound so-called "Jovian Lizards" are from Jupiter, but they're not lizards nor aliens, but humans driven off to Jupiter by the government.
- In the 1998 comic two-parter Marvel: Conspiracy, a reporter gradually discovers that practically all superheroes and supervillains ever since shortly after the very dawn of the Golden Age were the product of a black op called 'Control', founded to control extranormals, that got completely out of control to the extent the only surviving founder hasn't got a clue who, or even whether anyone is controlling it anymore. Of course, the Government tries to pass off his discovery as the ramblings of a madman before rubbing him out...
- Wolverine's backstory is filled with various government groups who always seem to be up to no good. The most famous of which, is Weapon-X, the Canadian/US research unit who initially gave him his adamantium skeleton and would later create Deadpool.
- In one two-part Amazing Spider-Man story during Eric Larson's run, Spidey teamed up with The Punisher to find out who was hording thousands of tons of cocaine but not selling it. It turned out that an agency in the actual U.S. Government (which one was not revealed) was behind this scheme. Worried that the economy's dependence on the Gold Standard might be a liability if gold were to lose value in a crisis, this agency was actually considering using cocaine as the new standard, reasoning that drugs always had value. While both Spider-Man and the Punisher knew this was a sick and misguided idea, they decided against exposing it; not only would it be hard for a judge to believe "a man in a mask like me and a walking gun shop like you" as Spidey put it, knowing about such a thing would hurt - if not destroy - what trust remained in America's government. (However, they did destroy the cocaine. Letting the conspiracy continue was not an option.)
- Prior to The New 52 reboot, Superman had Project 7734, headed up by General Sam Lane with the express purpose of squashing all Kryptonians. Including Superman.
- In said reboot, however, we have a new one in Superman Unchained: The Machine, home of Wraith and many alien technologies that have been incorporated into human operations. It was formed by Franklin D. Roosevelt in 1938, and has been a major force for the military ever since from behind the scenes as a Benevolent Conspiracy.
- The US government and army is having secret meetings with the Evronians and keeps the population in the dark even when they realize they are hostile in order to not spread large panic that would cripple their ability to fight bad. There have been a couple of tries to inform the public of it,but even Paperinik thinks it is better this way.
- The Simpsons: One issue has Homer and Lisa stumbling onto NASA's dark secret: After losing too many probes to Uranus, they decided to save money and effort by filming faked footage in the desert. Homer nearly blows the whole deal due to defacing their set with a golf-club, but the scientists are quickly able to bluff their way out.
- In Pokémon fanfic Clouded Sky, the government of Waytar, the region in which the story takes place, doesn't want anybody to know the truth about what's really beyond Waytar's Shield and are willing to use some underhanded methods to keep the secret from getting out.
- Celestia and Luna have several going in Diaries of a Madman. The first is perpetuating the myth that they control the sun and moon, the second being the covering up of "true magic". Nav's sudden disappearance later on in the story is thought to be the result of one as well, though it's clearly false from the reader's perspective.
- In Equestria: A History Revealed, according to the narrator, everything is a government conspiracy. They've been sending her subtle signs of the "true" history to toy with her. Little do they know, she'll reveal the "truth" to the world, whether the world wants to hear it or not.
- In Origins, a Mass Effect/Star Wars/Borderlands/Halo Massive Multiplayer Crossover, the Republic Intelligence Service seems to have subverted the entire Trans-Galactic Republic to the point where its favored Private Military Contractor can call up a shipyard and obtain hardware previously reserved for Spacelane Protection. It theoretically has a good reason for working to defeat the Alien Invasion Flood left unchecked is bad but its methods are rather brutal. Knocking out a democratic government doesn't bode well either, until you consider what the source material tends to think about democracy.
- The Mad Scientist Wars seems to set one of these up by introducing the mysterious M, The Men in Black-staffed Government Agency. Subverted in that it turns out that they have no ulterior motives - instead what they do is Exactly What It Says on the Tin, keeping Mad Scientists from destroying the planet, and helping them.
- Broken Souls features one in the Harry Potter universe's Ministry of Magic and the Moscow Clique, a powerful group in Russian wizarding politicians that have been controlling the country for nearly twenty years. A German reporter and his paper were following a story on them, investigating the possibility of them placing moles inside foreign governments in order to trade money for secrets and vice versa.
- In Ambience: Platoon (Moebius Four), there is an ultranationalist far-right faction within the Diet that is bent on returning control of the ship girls to Japanese hands, by force if need be. They try twice to assassinate Franklin and, when that fails, try to pull a Uriah Gambit on him. They eventually get their wish when an Abyssal attack on Okinawa incapacitates him.
- Ambience: A Fleet Symphony:
- the fact that it was Xenolith/The Abyssal who brought Lauren into the second F.L.E.E.T. Project, and that Lauren and Jeannie's escape from it led to an executive order for their capture by none less than the US President himself, implies two possibilities. Either the Inner Circle is directly in cahoots with the Feds, or they have deeply infiltrated the Feds. Neither possibility bears thinking about. It gets worse when Shoukaku's Abyssalised weapon reacts to Damon, suggesting a link between the Genesis Thesis Project and the Abyssals.
- Baltimore. As revealed in chapter 189, the Feds were working on something, and when it resulted in a mutation-inducing outbreak, quarantined the whole city far faster than they should have been able to, then hushed the whole thing up.
- The Pokémon fanfic The Power That's Inside shows a government that controls Gyms, Pokemon Centers, Poke Marts, all utilities...and marriages.
- Superwomen of Eva 2: Lone Heir of Krypton: SEELE is supposedly an UN Committee created to oversee NERV. In reality they control the UN.
- In Jewel of Darkness, it's revealed that Mad Mod was originally the head of the British Institute for the Prevention of Metahuman Crisis, a secret agency dedicated to "rehabilitating" Meta- and Super-criminals in order to prevent them from threatening British society. Then his peers found out he was planning on doing the same to key members of the government in order to take over the country, forcing him to go on the run.
- In the Naruto Fan Fic Team 8, there is one going on inside the Leaf Village between the Hyuuga Clan and many members of the Village Council, with the ringleaders seemingly being Hiashi and Danzo. Although their exact goals and motivations have not been clarified yet, it is heavily implied that they ordered the murder of Kurenai's former team and had been actively promoting hate against Naruto inside the village. Some characters, including the Hokage and Kurenai, are aware of its existence but have been unable to bring it down through legal means.
Films — Live-Action
- Chariot contains a failed government program designed to protect valuable citizens in the case of an attack on the United States. These "Valuable Citizens" consist of a truck driver from Beaumont, Texas, and a high-school drop-out, among other average Joes.
- H2O (the miniseries) — you think it's bad when Mars Needs Water; how about the US government!
- Three Days of the Condor — a CIA employee accidentally uncovers an illegal CIA conspiracy to start a war in the Middle East.
- The Parallax View — inspired by Who Shot JFK?; an Intrepid Reporter discovers a program to create 'lone gunman' assassins for political murders.
- Capricorn One — fake moon landing conspiracy, except this one is a trip to Mars.
- Oliver Stone's JFK is heavy with this, using true facts and made-up details to point to a big government conspiracy.
- The Men in Black may or may not actually be part of the government, but they act much like the usual Government Conspiracy does as they carry out their mission of maintaining the Masquerade. (And, contrary to the usual ways the trope is normally used, they're the good guys.) It seems they may not be anymore. They may have started as part of the government, but as K notes in the first movie, they don't report to anyone anymore, as "They ask too many questions," and are privately funded through owning the patents on several modern technologies.
- The 1998 The X Files film served to advance several of the TV series' plot arcs, notably the uncovering of massive government cover-ups.
- And the sequel pretty much ignored most of it.
- The Mel Gibson film Conspiracy Theory makes hot, sweaty monkey love to this trope.
- Big Game has one spring out of nowhere, although which government and what it's trying to achieve is awfully spoilerrific.
- The Cube film series:
- Subverted in the first Cube, where the protagonists at first speculate that the government is responsible for the mysterious cubical death maze and putting unwilling people in there. A character who is revealed to have worked on it explains that there is no grand master plan behind it and it sort of grew by itself without any oversight.
- Played straight by the sequels, where in Cube 2: Hypercube the hypercube is run by a secret cabal called Izon made up of military men and a Washington think tank, and in Cube Zero where the proto-cube is controlled by a future theocratic dictatorship.
- Hidden Agenda first has the cover-up of a human rights activist's murder in Northern Ireland, which itself was to cover up a larger conspiracy inside of the British government.
- In Captain America: The Winter Soldier, we find out that S.H.I.E.L.D., a multinational government agency that has appeared in pretty much every Marvel up to this point, is actually being controlled by a Neo-Nazi terrorist organization called HYDRA, reformed from it's days in WWII.
- In La Habanera, the American authorities in Puerto Rico conspire with a local businessman to cover up an outbreak of "Puerto Rico fever", so as to avoid damaging commerce on the island.
- Return of the Living Dead: Trioxin, the zombie-creating chemical, was originally developed by the U.S. government, and is only released once again in the first film through their carelessness by subcontracting its storage to people who don't know how to handle it. In the third movie, the military is still conducting trioxin experiments on fresh corpses.
- The Radix: Knights of Malta have occupied several USA government positions, using them for all kinds of shady business, including the hunt for the eponymous MacGuffin.
- In Adaptation. by Malinda Lo, The Government is keeping it secret that aliens have visited earth. The government has also experimented with alien technology to create Super Soldiers.
- This is the entire point of Nineteen Eighty-Four - a Government Conspiracy covering up the truth so thoroughly and so successfully that whatever it says effectively becomes the truth. Note that Orwell saw plenty of these in Real Life.
- David Wingrove's Chung Kuo has the Ministry, the only ministry without a name, that is tasked with hiding the truth about the past by all means possible.
- Isaac Asimov wrote a short story called "The Dead Past," where it turns out the government has a stranglehold on science in a massive conspiracy to prevent science from rediscovering an apparatus capable of looking into the past. It's also a glorious deconstruction, because it turns out that this is for humanity's own good, as "the past" starts at about a second ago, and the device can see anywhere in the world, thus making privacy obsolete. The protagonists fail to realize this until after they've managed to publicize the technology far and wide.
Araman: "Nobody knew anything, but you all just took it for granted that the government was stupidly bureaucratic, vicious, tyrannical, given to suppressing research for the hell of it. It never occurred to any of you that we were trying to protect mankind as best we could."
- In The Laundry Files books by Charles Stross, "The Laundry" is the name of a branch of the UK civil service responsible for dealing with incursions of monsters. Amongst other things, they make people who (accidentally or otherwise) attempt to summon an Eldritch Abomination or other Things Man Was Not Meant to Know disappear, either in the traditional way or by giving them a regular civil service job to keep them out of trouble. Definitely a case of a benign conspiracy, as nobody wants to end up timesharing their cortex with a demonic intelligence because some computer nerd accidentally wrote a summoning algorithm...
- In the first three of the Uglies series, the government lets extensive surgery happen on everyone to make them beautiful the moment they turn 16. It turns out during the operation your brain is messed with to make you vapid, stupid, and forgetful, but good at heart. This is a subversion as although everyone is stupid it has stopped wars, poverty, prejudice, and the environment is doing fine.
- Harry Potter
- Are the frequent villains in novels by James Byron Huggins.
- In his novel American Gods, Neil Gaiman includes the typical sinister government agents, complete with a "black train" that serves as a mobile prison. The real US government is not to blame, however. The conspiracy theorists themselves created the Spookshow through their fervent belief in its existence. Even though the agents don't show authorization, they successfully bully the local authorities into cooperating.
- MJ-12 (Majestic Twelve) in Little Green Men is responsible for simulating alien activity to keep American citizens alarmed enough to vote for lavish funding for military aerospace programs.
- In the Star Trek Novel Verse, the Zife Administration's actions on Tezwa, and their attempts to cover it up afterwards. In Star Trek: A Time to Kill, President Zife violated the Khitomer Accords with the Klingon Empire by illegally arming Tezwa, a neutral border world, as part of a contingency plan during the war against the Dominion. Later, the Tezwans use these weapons to attack the Klingons. Zife and his Chief of Staff, Koll Azernal, then order the planet occupied by Starfleet troops, ostensibly to help it rebuild from the Klingon counterstrike, but really to dismantle any evidence of Federation involvement. They also seek to frame another government for arming the Tezwans. Fake evidence is smuggled through the Defense Secretary via criminal organization the Orion Syndicate.
- In the Robert Harris novel Fatherland, the victorious-in-WWII Nazis conduct a murderous conspiracy to keep the Holocaust a secret.
- Illuminatus! introduces, inverts, subverts and turns it all rightish-side-up-again. It also (among many other things) asks what might happen when quite a lot of competing conspiracy theories are all active at the same time, with each having part of the power and no one group able to grab everything.
- Those That Wake has a corporate conspiracy, but it's close enough. They literally manufactured hopelessness until it grew a mind of its own.
- A Song of Ice and Fire: Two men. Two continents. At least Seven Kingdoms and a couple of city states and probably not just the one Crown with uncomfortable chair. One wide-ranging and free-wheeling plan to use them all. Isn't that right, Lord "the Spider" Varys and Illyrio Mopatis? It's not the largest in terms of the number of insigators or the complexity in its base premise, but... heavens above, it's large in scope! On the face of it, they are probably using the government of the Seven Kingdoms, various Essosi resources they have and their wits and outright gall to hand the Targaryens back the throne they lost. A loss which, all to likely, they probably played some small part in, once the situation came to light. (They have been playing each exiled Targaryen for all they are worth, while looking like support.) It's probably the biggest two-man con-job in the history of their world, as well.
- Petyr Baelish may have less of a wide-ranging plan and less well, but if you think he isn't using his position for his own ends... Well, there's this bridge for sale... You know the whole civil war? He instigated it while Varys was trying to put the breaks on the whole building mess for the timing of his own plan.
- Lady Dunstin is convinced the Citadel controls politics throughout the Seven Kingdoms for its own ends through the maesters that are oh-so useful to the lords they in turn rule through. Yes-no: they are deliberately directing knowledge and culture, not specifically politics. Most of them wish to end the reliance on magical lore.
- The Wandering has a government conspiracy on Neshi's homeworld, where the people in charge are under the influence of spirit beings known as Natasians, shaping events that lead to Neshi and a La Résistance group called the Jerusalemites infiltrating the Natasians' citadel to discover their secret plans.
- In The Southern Reach Trilogy, the titular Southern Reach is a secret government organization tasked with covering up the existence of the Eldritch Location Area X and sending in teams to explore it. The conspiracy actually extends to the members of the expeditions themselves: the maps they are given are deliberately incomplete and they are falsely informed about the numbering of their expedition.
- The plot of The Tenets of Futilism revolves around a conspiracy. After finding a senator hanging above his desk, a young woman named Sasha takes his journal out of undeniable curiosity. Reading one of its entries leads to her discovering the American government's plans to put excessive fluoride into the water supply, rendering the citizenry stupid, obedient, and impressionable. Turns out, all those people suspicious about fluoridation were on the right track. The substance does, in fact, have an effect on the mind, but only through very high dosages.
- The Paradox Trilogy has the Joint Investigatory Spatial Anomaly Task Force, a secret organization charged with battling Eldritch Abominations called phantoms. It was primarily founded by the Terran Republic, but because of the universal threat posed to all humans by phantoms, they are also allowed to wield near-absolute authority by the governments of territories which are independent from or even on hostile terms with the Republic.
- The City of Ember:
- The mayor, some of his guards, and storeroom worker Looper were secretly stealing and hording some rare items that they found in storage (which had supposedly run out long ago) rather than sharing them with the entire city.
- The plans set by the Builders themselves could qualify. Going through all the trouble of keeping the true contents of the box a secret. Or seeing to it that no one knew the history of the world leading up to the disaster in an attempt to start from a clean slate.
- Much of the plot of Newshound focuses on the discovery and investigation of a conspiracy involving abuse of the no fly list.
- Terra Ignota:
- A benevolent version is at the center of the first two books of the series. The supposedly disparate Hives are actually very closely intertwined through the relations their leaders have in Madame's brothel/church. Despite the general debauchery and the world's leaders literally being in bed with each other, they genuinely do value the safety and stability of the world over their own power, conducting secret negotiations and deals away from the public eye in the knowledge that should that ever come out, no matter how benevolent their intentions may be there would be a massive public outcry.
- A separate conspiracy in which the President of the Humanists, the Chief Director of the Mitsubishi and the Head of the European Parliament are involved is more ambiguous. Turns out that they've been behind a secret group of assassins conducting mathematically determined assassinations of certain individuals in order to keep the world's politics balanced, resulting in several hundred years of uninterrupted peace around the globe. On the other hand, their victims are innocents often uninvolved with politics and number in the thousands.
- 24 - seasons 5 and 7
- Babylon 5 has several governments from several worlds, many of them involved in several conspiracies. In particular, much of the show centers around the Centauri Republic's Deadly Decadent Court, with different noble Houses trying to outmaneuver each other, and the Earth Alliance, which proves to be host to numerous conspiracies between different parts of the government. In particular, the human protagonists are part of a conspiracy to prove that the President had his predecessor killed and to find out who is backing him, while the President is part of a very xenophobic conspiracy which is backed by a very powerful alien race. One character specifically refers to the heroes' conspiracy as a Conspiracy of Light.
- Dark Angel
- Dark Skies
- The Lone Gunmen: The series' pilot made a very good point regarding so-called "government conspiracies": while Conspiracy Theorists like the eponymous group love to blame all conspiracies on the entire government, it is usually just a small ruthless splinter faction that advances each of them. In other words, "government conspiracy" shouldn't be read "a conspiracy by the government" but "a conspiracy within The Government".
- The Prisoner
- Stargate SG-1, the protagonists are part of the conspiracy: aliens built the pyramids, their tech is stashed in military bases such as Area 51, and the United States Air Force is fighting a secret war with them in space.
- It is a conspiracy incorporating most of the major world governments, and probably every single space program. And what holds it all together? Nondisclosure agreements.
- The show includes two straighter examples, in the NID and later "The Trust", that are even more secret than above-mentioned programs. The first goes to far and gets taken down by the heroes, while the second one gets infiltrated by Goa'uld.
- Star Trek: Deep Space Nine, and later Star Trek: Enterprise, both feature an organization called Section 31, that's ambiguously part of the government. They're a group of Star Fleet officers who either work for the organization secretly, or just look the other way for them. They basically believe that "The end justifies the means", almost literally Utopia Justifies the Means, and are willing to commit Genocide when it comes to defending The Federation (or just Earth, in the Star Trek: Enterprise era). The crew of Deep Space 9 end up exposing them, after they fail to recruit Doctor Bashir into their organization.
- Section 31 were actually vital to achieving a happy ending for the Dominion War. Because it's explicitly stated (in "Statistical Probabilities", and by a Changeling admitting to their Salt the Earth strategy) that the Alpha Quadrant would have become a Crapsack World, had Odo not been able to use the cure to broker peace. This means that Section 31 did rescue the entire quadrant, and can be seen as Designated Villains with a point.
- Except that their plan wasn't to broker a peace with the Changelings; their plan was to Kill 'em All, and the virus they gave them probably led directly to the paranoid breakdown the Female Changeling suffered that caused her to order the xenocide of everyone on Cardassia, not to mention had Odo not broked the peace but the Changelings did remain infected, the Dominion may have still lost but they probably would have pulled a Taking You with Me on as many of their enemies as possible. So really, what Section 13 did counts as Nice Job Fixing It, Villain!, if a rare case where "fixing it" was actually a good- but unintended- outcome for them anyway.
- Section 31's name derives from Article 14, Section 31 of the Starfleet Charter, which makes allowances for bending Starfleet regulations in times of extraordinary threat. The organization, of course, promptly seized on that to motivate their existence (apparently reasoning that there always some extraordinary threat around or brewing).
- Section 31 were actually vital to achieving a happy ending for the Dominion War. Because it's explicitly stated (in "Statistical Probabilities", and by a Changeling admitting to their Salt the Earth strategy) that the Alpha Quadrant would have become a Crapsack World, had Odo not been able to use the cure to broker peace. This means that Section 31 did rescue the entire quadrant, and can be seen as Designated Villains with a point.
- Threshold, another one where the protagonists are part of the conspiracy. Actually, that's not quite accurate - the protagonists are the conspiracy.
- Torchwood, notable because the characters work for the conspiracy, and it's not run by the government per se but was established by the queen.
- Twin Peaks
- Ultraviolet, ditto.
- Also the Gerry Anderson live action series UFO, a 70's version of...
- The X-Files, in which the main storyline away from it's usual format dealt with a government conspiracy to cover-up the existence of extra-terrestrials.
- Heroes as of Volume 4, taking over when the previous (civilian) conspiracy was brought down.
- Person of Interest Northern Lights is a conspiracy between senior military and government officials, presidential advisers and members of Congress to carry out Sinister Surveillance in order to prevent terrorist attacks.
- Prison Break
- That Mitchell and Webb Look:
- Viciously parodied in a series of sketches such as this one, which highlights all the flaws in the idea by playing them completely straight, Circular Reasoning and all. For a start, the only reason the conspirators can come up with for concealing the existence of aliens is that it's "what governments do".
- There's also one about Princess Diana (their only concern about using the watertight method of getting the chaffeur drunk, chasing him with fifteen hired paparazzi on motorcycles, and hoping that Diana doesn't wear her seatbelt is that it will be obvious that it was planned) and one about the moon landing (especially diabolical, as it turns out that the only way to convincingly fake a moon landing involves building a spacecraft and landing it on the moon).
- At the end of the Diana sketch, it is revealed the conspiracy didn't kill Diana. The exact same watertight but obviously planned method happened on its own while they were drawing up their plan.
- In addition, the Moon landing hoaxers are simultaneously covering up, for unspecified reasons, the successful Mars landings!
- Smallville's ninth season featured Checkmate, a federal agency that sought to control all metahumans. Season 10 adds the psychopaths behind the Vigilante Registration Act, as well as the Suicide Squad, a group of former Checkmate agents out to oppose the government and anybody else who gets in their way.
- Buffy the Vampire Slayer had the Initiative in season four. They collect supernatural creatures (mostly demons) for "research". One episode of Angel reveals they existed during World War II and attempted to use the demons as weapons.
- In Nikita, there's Oversight, the group that Percy nominally reports to, but whom he's more or less separated from in order to run Division his way. When we first learn of their existence, they seem to just be a group of corrupt officials in the CIA, but then Percy meets with several of them in a restaurant and refers to them as "Admiral", "Senator", and "Joint Chief"note By the end of the first season, they've developed into a full blown Omniscient Council of Vagueness.
- The Shadow Line has Counterpoint, a conspiracy run by high-up police officers and MI5 to use drug money to top up the police pension pot.
- Season 4 of Lexx reveals that the Conspiracy Theorists are right: the ATF secretly controls the U.S. government from its Elaborate Underground Base beneath Washington, D.C. (And its current director is, in fact, Satan himself.)
- The Lottery has some kind of conspirisy going on. Details still to be revealed as time goes on.
- Blindspot has the mysterious Operation Daylight, and the cover up around it, which "Persecute Envoys" finally reveals in detail: the White House Chief of Staff brought together the White House's Deputy Political Director, Deputy Director Carter of the CIA, and Assistant Director Mayfair of the FBI, and tasked them with using illegally obtained NSA surveillance intelligence to further the government's aims in their respective fields (blackmailing political opponents, preventing terrorist attacks, and going after otherwise untouchable criminals), all while dressing up the intel to look legal. The cover up part comes in when a whistleblower exposed the NSA's surveillance program, at which point the Chief of Staff cut the other three loose to fend for themselves, denying all involvement. And of course, a clue to all of this in one of Jane's tattoos.
- More important to the Myth Arc is the project known as Orion, which Jane was part of at some point in her mysterious past. It eventually turns out to have been an offshoot of Daylight, the CIA having black-ops teams use the information provided by Daylight to carry out illegal assassinations. When it risked exposure, Carter had all the members (except Jane, who barely survived) killed to cover it up.
- Powers: In season 2, Heavy, the guy who killed Retro Girl is actually a rogue CIA operative, which they are very eager to cover up, even if it means letting Retro Girl's killer go free.
- The short-lived Agent X had, as one of its Story Arc plot points, a "shadow government" being formed by various high-ranking government officials (including the Speaker of the House) to carry out illegal covert operations to further their own personal agendas. It later turns out that they're just pawns of Big Bad Nicolas Volker who kills them once they're no longer necessary.
- Homeland: A group of government officials conspires to discredit and then assassinate the President elect in season six.
- Stranger Things proves to be largely centered on one of these (which you could see coming the minute you saw the words "Hawkins National Laboratory" in the first episode). In detail, the reason that weird stuff keeps happening in the otherwise unremarkable rural town of Hawkins, Indiana is that although the signs around Hawkins Laboratory say Department of Energy, the experiments are actually derived from an Alternate History version of the CIA's Project MKUltra. Unlike the historical project (for which see Real Life below), which mostly succeeded at introducing people like Ken Kesey to LSD and making some schizophrenics even more disturbed, the Stranger Things version actually succeeded in creating people with psionic powers they could use to spy on the Soviets. One of those people—Eleven—accidentally ripped a hole to an alternate dimension—the Upside-Down—while using these powers. Everything that happens in the series is a direct consequence of the experiments on Eleven.
- Happens basically every time we visit Ravnica or Fiora in Magic: The Gathering.
- Dark Matter, inspired by the popularity of The X-Files and the general profusion of millennialist conspiracy theories in the late 90s, was an eager Conspiracy Kitchen Sink setting where any government could be said to have some kind of secret agenda. Various US government organizations such as the CIA and FBI got their own profiles, while the US government in general was broadly assessed to be such a No Such Agency and alphabet agency-ridden mess that any number of conspiracies could arise from within. And that maybe such... obfuscations are intentional, and that there's a greater conspiracy that benefits from the illusion of jumbled incompetence.
- Delta Green is of similar vintage to Dark Matter, except with a Lovecraftian spin. The eponymous organization started as an anti-Mythos conspiracy of scattered US government personnel in-the-know about the creepy crawlies and how to fight them, but was eventually displaced by an actual Government Conspiracy set on trading away resources and citizens in exchange for alien technology.
- Metal Gear has The Philosophers in the US, China, and Russia. Succeeded by the PATRIOTS in the US. And they used memes to do it, the bastards.
- Floor 13, a game where you get to control a secret police force in the UK, trying to keep the government in power, and trying to prevent being revealed by pesky journalists.
- Played for laughs in Team Fortress 2 where the two teams one can play on, RED and BLU, are also multinational corporations secretly controlling every single government in the world, combating each other for world domination... or more specifically, control of some worthless gravel pits. Both are subdivisions of the same mother company, who maintains the RED-BLU feud to keep anyone from noticing.
- In Omikron: The Nomad Soul, it's revealed that the city of Omikron and it's government are actually controlled by demons, who rule from the shadows to prevent anyone from finding out their leaders' true nature. What sets off the protagonists to this is a demon who goes around killing people, and a police detective who thinks that the so-called "serial killer" is actually some sort of monster.
- The Malta Group in City of Heroes was formed by a bunch of politicians and businessmen annoyed that the Super Registration Act had been ruled unconstitutional. They formed an spread of cells of elite soldiers trained and equipped to take down and control superpowered individuals good or bad, by any means necessary. They're also paranoid enough to try to start a World War 3 with China.
- The Consortium in the Syphon Filter series.
- They're everywhere in Deus Ex.
- Alpha Protocol for sure in the eponymous game. It's hinted that there are probably others out there; in particular, one of the other factions, G22, is identified as possibly being a US government group. Alpha Protocol itself has had many names and identities through the years. One of which was "G19", remnants of which may have splintered off into G22.
- Inverted in Soviet Strike. The game seems to suggest that STRIKE, the organization you work for, is a multinational conspiracy going back decades. The coup was all their doing, and your subsequent rescue of Russian President Boris Yeltsin, was all an elaborate Batman Gambit designed to scare him into playing ball. One of the Audio Logs has the head of STRIKE telling President Clinton to his face that, when it comes to military matters, STRIKE calls all the shots.
- Final Fantasy XIII Galenth Dysley, leader of the Sanctum, is actually the fal'Cie Barthandelus and is trying to get our heroes to destroy Cocoon to bring back the Maker.
- The original Max Payne covered the aftermath of Project Valhalla, a US government-sponsored drug research that was Tested on Humans during the Gulf War. There is also the Inner Circle, a group of filthily rich old men who more or less control the US government (and are hinted to have been behind the Kennedy assassination).
- L.A. Noire The SRF is goading the stubborn families away from their uninsured homes with rigged vacation lotteries, sending an insane pyromaniac to burn the homes AND kill any family that hasn't left the house, and the insurance fraud profits of these homes are worth THE DIRT THEY'RE BUILT ON, and according to Cole, the actual worth of the houses is "Firewood. All of them.". The real money is in getting the whole set of lands, so that the SRF can build an entire freeway and commercial center and profit. Depending on your interpretation, while Kelso retalliates violently against the leaders of the SRF for killing families and recently retired war veterans, his silence of the evidence for the latter scheme implies that he supports the now-semi-purified growth of economic progress in L.A., even if it alienates any sense of friendship he had with Cole.
- Resident Evil is starting to go into this territory with the introduction of the Family in Resident Evil 6. According to in-game files, the Family have influenced global events since at least the Colonial era, and were even directly responsible for the nuking of Raccoon City.
- In [PROTOTYPE 2] a lategame cutscene has an agent from some government agency say that the plan to vivisect Maya Heller gets approval from Washington. Where exactly is unknown; however, Blackwatch was said in the first game to be so high up you had to look down to see the POTUS. The fact that Rooks with all his authority considers tangling with them unwise says that the rabbit hole goes really far down.
- Contra: Shattered Soldier has the Triumvirate, who is revealed by Lance Bean to be the ones truly responsible for provoking the Alien Wars as they had stolen a mysterious artifact from the aliens, known as the Relic of Moirai.
- Phantasy Star Online 2 has one, surprisingly: According to the leaders of ARKS, the series Big Bad Dark Falz was defeated. In truth, they couldn't defeat Dark Falz, so they sealed him instead. The leaders of ARKS are determined to keep the fact that Dark Falz is alive a secret, and will go as far as to assassinate members of their own organization to keep this secret.
- Fallout 2 features the Enclave, which started the Vault Project, created FEV, and after the bombs fall, went into hiding for over 150 years to regroup and consolidate its military forces and boost its technological superiority beyond anything that could possibly be available on the mainland. When they return they start performing covert operations on the mainland, such as using FEV to create new super mutants, selling energy weapons to a Mafia clan, and kidnapping Vault residents as part of their Evil Plan.
- Fallout 3 has the East Coast portion, cut off from the West Coast and led by President John Henry Eden a VAX super-computer that gained a mind of it's own and Colonel Autumn who plain on Using Project Purity and a modified strain of FEV to kill all "mutants" in the wasteland and their ace in the hole is the "Bradley-Hercules" orbital bombardment satellite commanded at the mobile base crawler at Adam's Airforce Base.
- Arcanum: Of Steamworks & Magick Obscura:
- A line of sidequests has the player uncovering a conspiracy involving inhumane breeding experiments at the hands of the leadership of the largest city on the continent. Despite your efforts, everyone involved in giving the quest is ultimately killed, and when you try to take the story to the press with the only evidence you have, it turns out the newspaper reporter you go to was a plant from the conspirators themselves, and the evidence vanishes forever. An NPC states that they occasionally let tidbits of information get out just so it all sounds like a crazy conspiracy theory.
- The main evil storyline reveals that the entire Panarii religion is a conspiracy, originally founded and still guided by an evil priest for the sole purpose is helping it's devil-figure return to this plane of existence. To achieve this, they have covered up a large number of events, including murdering one of the most notable and legendary Panarii saints and burying him in their supposed dead god's place.
- In Border Down, The First Approach were actually a fiction of the Earth officials behind the creation of SDF. SDF and RAIN were all just a ploy to (a) rip up Mars and force it back under Earth's rule...with Frank himself as a convenient fall guy for the disaster... and (b) design the ultimate battle machine — Red Wasps, the heavily armored versions of the Antares fighters that act as the 6-C and 6-D bosses. Even worse, everything but 6-C/D was a simulacrum fed to Frank to force him to ruin the space elevator...
- The Galactic Federation in Metroid: Other M was behind a conspiracy that created cybernetically-enhanced Zebesians, an android version of Mother Brain, and unfreezable Metroids, all enemies of Samus Aran.
- PAYDAY 2 It's implied that one was behind Hoxton's imprisonment, as during the Hoxton Breakout you need the clearance of the FBI Director to gather information, causing Hoxton to note that his case goes up to the top, higher than you would expect a mere heister's case to go. It's revealed that it was Hector that got Hoxton arrested since Hector, a criminal himself and had worked with the PAYDAY crew before the events of the game, was caught by the FBI and he agreed to a lesser sentence if he kept working with the PAYDAY gang as their contractor. This got Hoxton caught and probably would have gotten the others caught as well, but once the crew broke out Hoxton, they started to hunt down the rat that got Hoxton in jail and quickly discover that Hector was behind it. They track him down to an FBI safe house and kill him.
- In Evolve both Hub, the Earth-centered galactic superpower, and the gigacorps that run the Far Arm cover up the existence of the monsters while secretly studying and experimenting on them. This ultimately collapses, as neither of them actually created the monsters and they drop the charade when they realize full scale war is inevitable.
- Hatoful Boyfriend The Hawk Party discovered a more potent version of the H5N1 flu which eliminated all but about two percent of humanity and established St. PigeoNation's institute to do further research.
- In Phoenix Wright: Ace Attorney – Dual Destinies, seven years before the game's events the in-game-universe's national space organization of America, GYAXA, launched the HAT-1 Rocket onto a mission to send out a probe to collect asteroid samples. However, a spy working for an unknown government/organization sent a threat to the space center, stating that should the mission go ahead, they'd sabotage the ship. The US government insisted that terrorist threats should not make them surrender so the mission still went ahead. Just like the warning said though, the spy sabotaged the rocket, although the crew still managed to return safely to Earth despite impossible odds. As well as this, the day before the launch of HAT-1, a space center staff member was murdered by the same spy. The government however, covered up the real events behind both the HAT-1 incident and the murder, ordering that the murder investigation and conviction be rushed, so as to forever get rid of the terrorist behind the bombing of the HAT-1 from the public. They also forged a fake story for what "really happened" on to HAT-1, saying that the malfunctions were due to simple technical faults, causing a movie to be made called "The HAT-1 Miracle" (This is supposed to be the in-universe equivalent of the Apollo-13 Miracle). Seven years after all this occurred, aka in the game's final episode, the same spy ends up bombing GYAXA's Cosmos Space Center again, as well as a courtroom, leading to Phoenix Wright finally revealing the spy's identity and working out the conspiracy behind the HAT-1 Miracle.
- Mag Isa — we have a bunch of guys sitting around the table who seem to have control of the police forces of the nation... and other things that can be used for more evil against the people...
- Hinted at in this Sluggy Freelance strip. Several people, two of them government agents, are murdered, and when another agent asks a lot of questions about it, the Internal Affairs guys are very emphatic about her keeping quiet.
Agent: You seem more concerned about me than about what happened here.
Internal Affairs: "Seem?"
- The government conspiracy in Fans!, whilst undoubtedly secretive and ruthless, is eventually revealed as being non-malevolent in nature (if not without it's corrupt side), in fact sharing the same goals (if with more pragmatic and darker methods) as the heroes.
- A major plot point in Dan and Mab's Furry Adventures . A council has been planning to use Jyryas... somehow. Same for Dan, but that's with his mom and every other major Cubi apparently.
- In Schlock Mercenary, the United Nations of Sol, the government of most of the human race, is not the most scrupulous of governments. Some of the top military, espionage, and civilian leaders have been perpetrating a conspiracy with the end goal of making themselves immortal, but did a lot of other bad stuff along the way. The Toughs run headfirst into the conspiracy several times, and only survive by having very powerful friends plus some Fake Memories.
- In Shifters the majority of humanity doesn't know that Shifters, Vampires, or any of the other Veil Races exist due to the The Veil, which the Government is an integral part of.
- A Girl and Her Fed approaches this from an interesting angle. As Speedy put it: "You want to know the real definition of a conspiracy? One guy makes a mistake, and six guys clean it up." Considering he's a bio-engineered super-intelligent talking koala, he knows what he's talking about. The story revolves around "the chip," a brain implant given to a number of federal agents allowing them to use Augmented Reality technology. But it went horribly wrong, as the agents found the interface extremely annoying, it could not be turned off for hours after activation, and was prone to being turned on seemingly at random. Several hundred of the government's best and brightest basically became walking zombies, as they intentionally deadened their emotions to keep the chip at bay (also, the government-supplied drugs helped). As Speedy noted, the whole thing was a massive embarrassment, and the government did everything they could to bury it. The interesting part is that was all exactly as planned. The chips were a lot more powerful than anyone except the original designers realized, but wouldn't function without a biological component. By creating the annoying emotion-activated interface and supplying lots of drugs, they trained the agents to turn themselves into human robots. And by letting everyone think the program was a failure, the government covered up the conspiracy without even realizing it.
- xkcd concludes that if there's any secret organization controlling the US government, they're apparently pretty damn incompetent at it, as seen in an open letter following the 2013 government shutdown: "Can you please get your shit together? This is embarrassing."
Alt Text: Are you ok? Do you need help?
- Skin Horse: Played for Laughs twice over.
- First, we have Project Skin Horse, a top-secret government black-ops welfare service. They're dedicated to getting government aid for nonhuman sapients, typically those created by mad science. The primary reason they remain a secret despite incompetency all around is because normal people have a massive Weirdness Censor about things like talking dogs and zombies.
- Second is Anasigma, Dr. Lee's organization. They're far more competent than Skin Horse, but also bizarrely and unnecessarily creepy. They have protocols for vaporizing agent's underwear drawers, are obsessed with well-shined shoes to the point of killing their own agents for shining their shoes wrong, have a base full of literally thousands of death traps, and are trying to eliminate or exploit all non-human sapients. In the end, it turns out that the secret behind their success was a portal that let them view alternate universes, letting them predict the future with a high degree of accuracy.
Tip: What is Anasigma?
Dr. Lee: I wish I knew. When I started to work there, I thought it was a biotech firm. But biotech research is just one piece of a very big pie. Weapons development, mercenary services, espionage... I think we're the shadow government.
Tip: No, we're the shadow government.
Dr. Lee: I mean the shadow government that actually gets things done.
Tip: Oh. Those guys.
- Played in Kim Possible as the U.S. Government had known for a long time that aliens are real, but purposely disseminated this fact as a conspiracy to make the general public believe that a Conspiracy Theorist seems like a paranoid individual and discredit the theory. Lampshaded by Ron on the questionable logic of this plan given that everyone already suspected that the U.S. Government was hiding evidence for aliens.
- Severely subverted in the South Park episode "Mystery of the Urinal Deuce," where the boys' investigation into the titular restroom incident leads them to uncover the truth about 9/11. Most Americans are smart enough to comprehend that 9/11 was done by "a bunch of pissed-off Muslims," but the rest are "retarded" and need a conspiracy to believe in. So the US government obliges them, creating websites and giving the impression that it's capable of carrying out such an enormous False Flag Operation. Or in other words, the 9/11 conspiracy is the government conspiracy.
- Subverted in the Superman: The Animated Series episode "Where there's Smoke"; the villains work for the government, but the project is unauthorized.
- Project Cadmus in Justice League Unlimited aimed to destroy the Justice League if they ever went rogue like the Justice Lords. It came close to becoming a Self-Fulfilling Prophecy, but the Justice League discovered the Man Behind the Man.
- Avatar: The Last Airbender has the Dai Li, who more or less run Ba Sing Se and have kept the entire 100-year war a secret from the citizens (including the Earth King), brainwashed anyone who speaks of the war (including Jet) and were eventually taken over by Azula when the Gaang had Long Feng, the leader, arrested.
- On The Simpsons, the Republican Party is in cahoots with the FCC; the Fox network deliberately airs programs with morally reprehensible content so that they will be fined by the FCC, with the fines being funneled to the Republican Party. Kent Brockman says everyone in the entertainment business knows this, but no one is brave enough to report the scam; after he's fired, Lisa convinces him to gain that bravery, but he sells out after they offer to give him his job back with a 50% raise. (This is, of course, one of many examples of the show's Biting-the-Hand Humor.)
- The Star vs. the Forces of Evil episode "Butterfly Trap" reveals that the Magic High Commission conspired alongside Eclipsa's ex-husband and king of Mewni to replace Eclipsa's bastard, half-monster baby daughter (Meteora/Miss Heinous) with a peasant Mewman baby girl (Festivia), all because they couldn't allow someone of monster descent to take Mewni's throne. Since then, the Commission has gone through great lengths to make sure that Eclipsa's daughter would have her existence erased and then replaced by Festivia from all historical records.
- Real Life examples are, of course, objects of much debate, but the handful of confirmed conspiracies traceable to the United States government is large enough to be depressing. Notable examples include:
- Watergate, of course, is the most well-known, so much that most modern-day scandals have "-gate" added to the end as a suffix.
- Teapot Dome was likely the most notorious before Watergate, an executive order Harding signed that was, in effect, the result of bribery in order to gain leases on oil-rich lands. While many were arrested and convicted, Harding was never officially accused of anything—chiefly because he seems not to have known about the illegal activity that put the order on his desk, but also in part because he died before anyone but the conspirators knew what had happened.
- COINTELPRO, an FBI task force created in the mid-50s to sabotage, harass, and some even say murder "subversive" organizations, including Civil Rights groups, workers' unions, anti-war protests, the Black Panthers, and the Ku Klux Klan. Discontinued in the early 70s, but you'll find plenty of people who say otherwise.
- The Iran-Contra Affair, an elaborate three-way deal between the CIA, Iran, and a band of Nicaraguan rebels. To be brief, the CIA sold weapons to Iran in exchange for cash and hostages, then funneled much of the proceeds into the pockets of the Contras—all well and good, if it weren't illegal.
- And of course the stories of the U.S. government's (specifically the CIA's) involvement in the trafficking and selling of cocaine through third parties, which supplied the drug dealers on the street and which caused the crack epidemic that hit the inner cities hard. Supposedly it helped fund illegal operations elsewhere, like the above Contras. While no one has proven the CIA directly was involved with and/or knew about the drug smuggling, it seems clear they didn't much care to know or stop it either.
- Probably one of the sickest conspiracies ever was the Tuskegee Experiment, wherein US Health Officials willingly and readily prevented African-American men from getting aid for syphilis, which even at the time the experiment was performed was treatable, just to see what effect the disease would have as time went on (never mind the fact that humanity had known about syphilis and its effects for centuries, if not longer).
- Considering how popular the eugenics movement was at the time, this is far from surprising. The Tuskegee Experiment was also far from the worst of them performed by the US government, let alone some of the experiments which were considered highly unethical even by the looser standards of medical ethics, which were performed by doctors for medical research without government funding. And let's not even start on the role of the states in eugenics (look up the Eugenics Board of North Carolina if you want to be particularly horrified)...
- Project MKULTRA is a rather well known one. The CIA attempted to use LSD, other drugs, and hypnosis to develop some form of mind control.
- They also used ridiculously damaging amounts of electroshock, sensory deprivation and other experimental treatments on its subjects to try to inform brainwashing. One of the more well-known theories is that the ultimate goal was in fact to set up dissociative identities in the subconscious of certain individuals that could be activated at any time, override the primary personality, and be completely obedient and subservient (usually for purposes of assassination). Yes, the CIA apparently wanted to create a Manchurian Agent. Whether this is true or not, there is strong evidence, as well as scattered victim testimony, that they used a large number of psychiatric patients as guinea pigs for experimentation - often without consent - for 2 primary reasons: 1) No one believes a crazy person, and 2) people with psychosis and complex neurosis are easier to break, with personality integrity already being fragile, and are subsequently much easier to reformat and shape. Unfortunately, determining whether a schizophrenic who believes they were brainwashed by the CIA is reporting reality or fiction sort of proves the point. For further conspiracy, there is widespread belief among conspiracy-theorists and ex-CIA agents alike that the idea that MKULTRA has in fact been stopped is misinformation, and the project continues in various modernised forms to this day.
- Interestingly, the only drug that proved remotely useful for the purpose was simple pot, and it wasn't the CIA that did it, but the FBI. They spiked an arrested gangster's cigarettes with THC (it was not unusual then to give a perp cigarettes, since pretty much everyone was a smoker), and he proceeded to spill the beans on some heist or other. Of course, even THC proved to be prohibitively unpredictable.
- Using alcohol for exactly that purpose (usually by covert agents of the government) is centuries-old, thus the Latin idiom In Vino Veritas. Aleksandr Solzhenitsyn describes it as a fairly common procedure used by NKVD to get signed confessions (usually fake, as many political prisoners were in fact innocent). He notes that it was particularly effective in the case of prisoners unaware that malnutrition greatly decreases their resistance to toxins.
- The various attempts to assassinate or discredit Fidel Castro that the CIA carried out in the 1950s and 1960s. Everything from attempting to sabotage his diving equipment to poisoning / drugging his cigars (often with some form of psychotropic drug — again with the psychotropic drugs...) to attempting to create some kind of chemical that would cause his hair to fall out, thus ridding him of his iconic beard. You couldn't make some of these things up.
- Similarly, Operation Northwoods, a series of proposals to drum up support for a war against Castro's Cuba through a False Flag Operation against U.S. military and civilian targets, among which was included a "Communist Cuban terror campaign in the Miami area, in other Florida cities and even in Washington". While the plan was rejected by President Kennedy and none of the proposals ever became operational, it has been used by conspiracy theorists ever since its declassification and release as evidence that there are elements within the U.S. government who have no qualms over deceiving and even attacking citizens.
- The CIA has been involved in several revolutions all around the world since the 1950's - most infamously Iran's 1953 coup, but also Guatemala in '54, the attempted '58 revolution in Indonesia, the failed Bay of Pigs invasion of Cuba in '59, South Vietnam in '63, and so forth. There's also coups in which the CIA is suspected of merely offering tacit support for the plotters, such as Syria in '49, Brazil in '64, and Turkey in 1980. And of course there are the things the CIA has gotten involved in that we don't know about yet.
- During Prohibition, many speakeasys were supplied by stealing alcohol intended for industrial uses. The FBI responded by covertly poisoning the industrial alcohol en masse. What followed was called "The Chemists War", a battle between bathtub Chemists trying to remove the poisons and the FBI adding increasingly deadly concoctions to the industrial alcohol supply.
- The Great Purge orchestrated by Nikolai Yezhov's NKVD on the orders of Joseph Stalin was officially a "swift retribution for the assassination of Sergei Kirov, beloved comrade and close friend of Stalin, an act indicating a reactive conspiracy in the highest echelons of Soviet government". Stalin was baffled and angry at the killing, and yet more baffled when the official investigation (accurately, as we now know) determined that Kirov really had been murdered by a run-of-the-mill embittered, gun-toting loony (Leonid Nikolaev) when Kirov's bodyguard had been distracted. For a whole host of reasons 1935 was shaping up to be a good year to execute 850k potentially-troublesome people and imprison another million, so even though Stalin knew it was a lie he took the opportunity to claim that Kirov had been assassinated by 'rightist elements' to justify doing so.
- Nikita Khrushchev was the first senior Soviet politician to officially endorse an alternative conspiracy surrounding Kirov's death, which also claimed that it had been an assassination but said that it was Stalin who had ordered him killed. Unfortunately for Khruschev, the investigation he ordered into the assassination also concluded that Nikolayev did it - so when Khruschev spread rumors about Stalin being behind Kirov's murder, he had to do so with no actual evidence. Even so, Stalin's reputation ensured that many in The West believed Khruschev's tenuous claims right up until the mid-1990s, when NKVD archives (including Nikolaev's diary, which is a tome of pure crazy) burst that particular bubble. Some people in the former USSR still believe that Stalin was behind it to this day, unsurprisingly.
- Imperial Japan. The various generals and military officials would often double cross one another, ignore orders from Tokyo, lie to their superiors, and even start whole wars complete with a False Flag Operation. The reasons for this varied wildly: some wanted to increase their personal standing in Japan. Some wanted to bring more political power to their particular province. Some wanted to increase funding to their branch of the military. Budget disputes between the Army and the Navy even resulted in an invasion of the Soviet Union and possibly the declaration of war on the United States. Certain units of the military, such as the Kwantung Army, also acted completely independently of the main government and any officer with a higher rank than their current commander. This was also the period of government by assassination in which doves in the government were mostly assassinated throughout the 1930s such that by the war there were virtually none left in power. With all of these figures competing for influence, it's hard, even now, to determine who was really in charge of it all. The Emperor was supposed to have all the power, but the military could and would invade countries without even informing him. This wasn't helped by the US occupation forces intentionally muddling up the history of the government at the time; they needed the Emperor alive to make sure the occupation went peacefully, and tried to portray everything as the fault of the Prime Minister.
- Kei cars and other laws regarding vehicle size are secretly Japan's government conspiracy since the postwar days. Originally, the kei cars were designed to be an alternative transport method to motorcycles, but the government has been promoting them by giving them tax breaks and subsidies. With the government's ridiculous tax penalties to large vehicles, these small cars received many benefits and all Japanese car makers have been backed by government budgets until recent times. However, this also turned Japan into a Galapagos automotive market, effectively closing the foreign competition out, and killed off many larger cars as well, with the help of unique safety and emission laws that are not compatible with global standards. Now, some few government officials have warned that kei cars are starting to hurt the automotive industry in Japan, calling them a waste of research and development costs, despite the general public in Japan loving these small cars.